[gmx-users] soft-core potential in combination with PME (sorry, again)
gmx3 at hotmail.com
Fri Apr 13 18:29:23 CEST 2007
>From: "David Mobley" <dmobley at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] soft-core potential in combination with PME
>Date: Fri, 13 Apr 2007 09:18:21 -0700
>Berk and all,
>>I don't understand what David Mobley meant exactly.
>>There is no Coulomb singularity with soft-core.
>>Maybe one could have an unfortunate situation where the LJ
>>is already very soft, but the Coulomb not very soft,
>>which could lead to instabilities.
>>But I have never encountered this.
>Anytime I do a simulation where I turn of both coulomb and LJ
>interactions at the same time, I run into this problem. Sometimes it's
>worse than others. Maybe it's because the 1/r^12 and 1/r have
>different r-dependencies? I don't know.
>I suspect the issue partly is just what's optimal: The soft core
>parameters that would be optimal for modifying Coulomb interactions
>are not optimal for modifying LJ interactions, and vise versa. So if
>you use soft core settings that give you a smooth transformation for
>LJ interactions, you do too much or too little smoothing of the
>Coulomb interactions and introduce large Coulombic forces. On the
>other hand, if you pick soft core parameters that are good for Coulomb
>interactions, you end up with large LJ forces. (For example, Coulomb
>transformations are nearly optimal with LINEAR lambda scaling
>(sc-alpha=0), but that doesn't work *at all* for LJ transformations.
>If I remember correctly, basically what the Anwar paper tries to
>achieve is separately smoothing the two. You could probably accomplish
>the same thing by allowing separate sc-alpha and sc-power for Coulomb
>and LJ interactions so they can be tuned separately.
>So, while formally using soft core for Coulomb removes the
>singularity, in practice I think the forces are still large enough
>(when using soft core parameters are tuned for LJ interactions) that
>instabilities result (at least for the stuff I do, with the force
>field I use). Hence my recommendation to do two stages.
>Anecdotally, I should mention that a bunch of different people have
>e-mailed asking me about various problems they're having where they
>get unexpected free energies, etc. I suggest they do the Coulombic and
>LJ parts separately, and invariably they write back that it works much
I agree that doing it separately is more efficient and causes less trouble.
That would also be my advice.
I can only say that I have never encountered instabilities,
although I have had systems where I needed a lot of sampling
because of inconvenient Coulomb vs LJ soft-core paths.
I have not read Anwar's paper, but I think it would be impossible
to devise a different Coulomb and LJ scaling that would solve
the problem, as you also have to deal with neighboring atoms.
The main problem is usually in hydrogen bonds involving hydrogens bound
to other atoms.
Live Search, for accurate results! http://www.live.nl
More information about the gromacs.org_gmx-users